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Chkdsk results
Idiot me restarted (hard reset) the computer when it was stuck loading drivers - didn't realise it was running chkdsk in the background - when it rebooted it stopped at the same place but left it there for 15 mins or so and it finished successfully.
In my DOS days you used to be able to see the progress of chkdsk.

Thanks again for all the help. I won't worry about the superfetch then.

Since doing the chkdsk I have not had anymore issues for the last 3 days so I will flag this as the answer and mark this as solved.

Sounds like there could have been some corruption when cloning but not bad enough for it to present itself until now.
I will keep my eye on things and if need be, if i can't continue this thread, start a new one linking this thread.

Just to prevent this kind of issues in the future, I recommend to run the chkdsk with /r switch every once in a while on each partition (like once in a month).
/r includes the /f,
- /f fixes errors on the disk,
- /r locates bad sectors, attempts to recover readable data and includes additional analysis of physical disk errors.

A system file check, sfc /scannow command, after updates from Windows Update is also recommended
SFC can also be done monthly, because of the update cycle Microsoft uses (every 2nd tuesday of the month)

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